Starting phenix.real_space_refine on Thu Feb 22 19:57:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl9_24522/02_2024/7rl9_24522_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl9_24522/02_2024/7rl9_24522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl9_24522/02_2024/7rl9_24522.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl9_24522/02_2024/7rl9_24522.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl9_24522/02_2024/7rl9_24522_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl9_24522/02_2024/7rl9_24522_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 180 5.16 5 C 22098 2.51 5 N 6192 2.21 5 O 6726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 304": "OD1" <-> "OD2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A GLU 491": "OE1" <-> "OE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A GLU 704": "OE1" <-> "OE2" Residue "A GLU 730": "OE1" <-> "OE2" Residue "B ASP 304": "OD1" <-> "OD2" Residue "B PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B GLU 491": "OE1" <-> "OE2" Residue "B PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 534": "OE1" <-> "OE2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "B GLU 704": "OE1" <-> "OE2" Residue "B GLU 730": "OE1" <-> "OE2" Residue "C ASP 304": "OD1" <-> "OD2" Residue "C PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C GLU 491": "OE1" <-> "OE2" Residue "C PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 534": "OE1" <-> "OE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C GLU 704": "OE1" <-> "OE2" Residue "C GLU 730": "OE1" <-> "OE2" Residue "D ASP 304": "OD1" <-> "OD2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "D GLU 491": "OE1" <-> "OE2" Residue "D PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 534": "OE1" <-> "OE2" Residue "D GLU 546": "OE1" <-> "OE2" Residue "D GLU 704": "OE1" <-> "OE2" Residue "D GLU 730": "OE1" <-> "OE2" Residue "E ASP 304": "OD1" <-> "OD2" Residue "E PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 466": "OE1" <-> "OE2" Residue "E GLU 491": "OE1" <-> "OE2" Residue "E PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 534": "OE1" <-> "OE2" Residue "E GLU 546": "OE1" <-> "OE2" Residue "E GLU 704": "OE1" <-> "OE2" Residue "E GLU 730": "OE1" <-> "OE2" Residue "F ASP 304": "OD1" <-> "OD2" Residue "F PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 466": "OE1" <-> "OE2" Residue "F GLU 491": "OE1" <-> "OE2" Residue "F PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 534": "OE1" <-> "OE2" Residue "F GLU 546": "OE1" <-> "OE2" Residue "F GLU 704": "OE1" <-> "OE2" Residue "F GLU 730": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 35220 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 5816 Classifications: {'peptide': 744} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 703} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 5816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 5816 Classifications: {'peptide': 744} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 703} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 5816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 5816 Classifications: {'peptide': 744} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 703} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 5816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 5816 Classifications: {'peptide': 744} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 703} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 5816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 5816 Classifications: {'peptide': 744} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 703} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 5816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 5816 Classifications: {'peptide': 744} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 703} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.05, per 1000 atoms: 0.48 Number of scatterers: 35220 At special positions: 0 Unit cell: (166.402, 181.83, 115.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 180 16.00 P 24 15.00 O 6726 8.00 N 6192 7.00 C 22098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.26 Conformation dependent library (CDL) restraints added in 7.0 seconds 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8316 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 192 helices and 18 sheets defined 38.4% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.29 Creating SS restraints... Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 86 through 89 removed outlier: 3.862A pdb=" N ARG A 89 " --> pdb=" O ARG A 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 89' Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 191 through 199 removed outlier: 4.147A pdb=" N SER A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 225 removed outlier: 4.154A pdb=" N GLU A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 230 No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.641A pdb=" N ARG A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 333 Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 374 through 384 removed outlier: 3.566A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 383 " --> pdb=" O GLU A 379 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS A 384 " --> pdb=" O ILE A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 408 through 426 removed outlier: 3.757A pdb=" N ALA A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG A 424 " --> pdb=" O LEU A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 449 through 458 Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 483 through 491 removed outlier: 4.050A pdb=" N ARG A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 498 No H-bonds generated for 'chain 'A' and resid 495 through 498' Processing helix chain 'A' and resid 500 through 506 removed outlier: 3.503A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 removed outlier: 3.844A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 552 removed outlier: 3.552A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 568 removed outlier: 3.673A pdb=" N GLU A 561 " --> pdb=" O ASN A 558 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS A 565 " --> pdb=" O ILE A 562 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 567 " --> pdb=" O ASP A 564 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN A 568 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 585 removed outlier: 4.453A pdb=" N ILE A 582 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS A 584 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 650 through 660 removed outlier: 4.054A pdb=" N VAL A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 removed outlier: 3.629A pdb=" N MET A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 706 removed outlier: 3.513A pdb=" N GLU A 689 " --> pdb=" O ALA A 685 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 removed outlier: 4.110A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 763 removed outlier: 4.093A pdb=" N LYS A 754 " --> pdb=" O ASN A 750 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR A 755 " --> pdb=" O ASP A 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 86 through 89 removed outlier: 3.861A pdb=" N ARG B 89 " --> pdb=" O ARG B 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 89' Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 191 through 199 removed outlier: 4.146A pdb=" N SER B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 225 removed outlier: 4.154A pdb=" N GLU B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET B 219 " --> pdb=" O GLN B 215 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 230 No H-bonds generated for 'chain 'B' and resid 227 through 230' Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 281 through 295 removed outlier: 3.640A pdb=" N ARG B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 333 Processing helix chain 'B' and resid 355 through 358 Processing helix chain 'B' and resid 374 through 384 removed outlier: 3.565A pdb=" N GLU B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 383 " --> pdb=" O GLU B 379 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS B 384 " --> pdb=" O ILE B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 408 through 426 removed outlier: 3.758A pdb=" N ALA B 412 " --> pdb=" O GLY B 408 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 442 No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 449 through 458 Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 491 removed outlier: 4.051A pdb=" N ARG B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU B 488 " --> pdb=" O ASP B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 498 No H-bonds generated for 'chain 'B' and resid 495 through 498' Processing helix chain 'B' and resid 500 through 506 removed outlier: 3.503A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 535 removed outlier: 3.845A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 552 removed outlier: 3.552A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 568 removed outlier: 3.673A pdb=" N GLU B 561 " --> pdb=" O ASN B 558 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS B 565 " --> pdb=" O ILE B 562 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B 567 " --> pdb=" O ASP B 564 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN B 568 " --> pdb=" O LYS B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 585 removed outlier: 4.452A pdb=" N ILE B 582 " --> pdb=" O LEU B 579 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS B 584 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 609 Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 631 through 633 No H-bonds generated for 'chain 'B' and resid 631 through 633' Processing helix chain 'B' and resid 650 through 660 removed outlier: 4.055A pdb=" N VAL B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 678 removed outlier: 3.629A pdb=" N MET B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 706 removed outlier: 3.512A pdb=" N GLU B 689 " --> pdb=" O ALA B 685 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE B 690 " --> pdb=" O ASP B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 removed outlier: 4.110A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 763 removed outlier: 4.093A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR B 755 " --> pdb=" O ASP B 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'C' and resid 86 through 89 removed outlier: 3.861A pdb=" N ARG C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 86 through 89' Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 191 through 199 removed outlier: 4.147A pdb=" N SER C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 198 " --> pdb=" O GLU C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 225 removed outlier: 4.154A pdb=" N GLU C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N MET C 219 " --> pdb=" O GLN C 215 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL C 220 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 230 No H-bonds generated for 'chain 'C' and resid 227 through 230' Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 281 through 295 removed outlier: 3.640A pdb=" N ARG C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU C 291 " --> pdb=" O ARG C 287 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 333 Processing helix chain 'C' and resid 355 through 358 Processing helix chain 'C' and resid 374 through 384 removed outlier: 3.566A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS C 384 " --> pdb=" O ILE C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 Processing helix chain 'C' and resid 408 through 426 removed outlier: 3.757A pdb=" N ALA C 412 " --> pdb=" O GLY C 408 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 423 " --> pdb=" O ALA C 419 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG C 424 " --> pdb=" O LEU C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 442 No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing helix chain 'C' and resid 449 through 458 Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 483 through 491 removed outlier: 4.051A pdb=" N ARG C 487 " --> pdb=" O GLU C 483 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 498 No H-bonds generated for 'chain 'C' and resid 495 through 498' Processing helix chain 'C' and resid 500 through 506 removed outlier: 3.504A pdb=" N PHE C 506 " --> pdb=" O LYS C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 535 removed outlier: 3.844A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 552 removed outlier: 3.552A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 568 removed outlier: 3.672A pdb=" N GLU C 561 " --> pdb=" O ASN C 558 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS C 565 " --> pdb=" O ILE C 562 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG C 567 " --> pdb=" O ASP C 564 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN C 568 " --> pdb=" O LYS C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 585 removed outlier: 4.453A pdb=" N ILE C 582 " --> pdb=" O LEU C 579 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS C 584 " --> pdb=" O SER C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 609 Processing helix chain 'C' and resid 626 through 628 No H-bonds generated for 'chain 'C' and resid 626 through 628' Processing helix chain 'C' and resid 631 through 633 No H-bonds generated for 'chain 'C' and resid 631 through 633' Processing helix chain 'C' and resid 650 through 660 removed outlier: 4.053A pdb=" N VAL C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 678 removed outlier: 3.629A pdb=" N MET C 678 " --> pdb=" O PHE C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 706 removed outlier: 3.512A pdb=" N GLU C 689 " --> pdb=" O ALA C 685 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 742 removed outlier: 4.111A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 763 removed outlier: 4.094A pdb=" N LYS C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR C 755 " --> pdb=" O ASP C 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 48 Processing helix chain 'D' and resid 86 through 89 removed outlier: 3.861A pdb=" N ARG D 89 " --> pdb=" O ARG D 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 86 through 89' Processing helix chain 'D' and resid 136 through 138 No H-bonds generated for 'chain 'D' and resid 136 through 138' Processing helix chain 'D' and resid 191 through 199 removed outlier: 4.147A pdb=" N SER D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D 198 " --> pdb=" O GLU D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 225 removed outlier: 4.154A pdb=" N GLU D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET D 219 " --> pdb=" O GLN D 215 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL D 220 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 227 through 230 No H-bonds generated for 'chain 'D' and resid 227 through 230' Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 281 through 295 removed outlier: 3.640A pdb=" N ARG D 287 " --> pdb=" O GLU D 283 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU D 291 " --> pdb=" O ARG D 287 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 333 Processing helix chain 'D' and resid 355 through 358 Processing helix chain 'D' and resid 374 through 384 removed outlier: 3.566A pdb=" N GLU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS D 384 " --> pdb=" O ILE D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'D' and resid 408 through 426 removed outlier: 3.757A pdb=" N ALA D 412 " --> pdb=" O GLY D 408 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE D 423 " --> pdb=" O ALA D 419 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG D 424 " --> pdb=" O LEU D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 442 No H-bonds generated for 'chain 'D' and resid 439 through 442' Processing helix chain 'D' and resid 449 through 458 Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 483 through 491 removed outlier: 4.051A pdb=" N ARG D 487 " --> pdb=" O GLU D 483 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU D 488 " --> pdb=" O ASP D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 498 No H-bonds generated for 'chain 'D' and resid 495 through 498' Processing helix chain 'D' and resid 500 through 506 removed outlier: 3.504A pdb=" N PHE D 506 " --> pdb=" O LYS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 535 removed outlier: 3.844A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 552 removed outlier: 3.552A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 568 removed outlier: 3.673A pdb=" N GLU D 561 " --> pdb=" O ASN D 558 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS D 565 " --> pdb=" O ILE D 562 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG D 567 " --> pdb=" O ASP D 564 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN D 568 " --> pdb=" O LYS D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 585 removed outlier: 4.453A pdb=" N ILE D 582 " --> pdb=" O LEU D 579 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS D 584 " --> pdb=" O SER D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 609 Processing helix chain 'D' and resid 626 through 628 No H-bonds generated for 'chain 'D' and resid 626 through 628' Processing helix chain 'D' and resid 631 through 633 No H-bonds generated for 'chain 'D' and resid 631 through 633' Processing helix chain 'D' and resid 650 through 660 removed outlier: 4.053A pdb=" N VAL D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 678 removed outlier: 3.629A pdb=" N MET D 678 " --> pdb=" O PHE D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 706 removed outlier: 3.511A pdb=" N GLU D 689 " --> pdb=" O ALA D 685 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D 690 " --> pdb=" O ASP D 686 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 removed outlier: 4.110A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 763 removed outlier: 4.093A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR D 755 " --> pdb=" O ASP D 751 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 48 Processing helix chain 'E' and resid 86 through 89 removed outlier: 3.861A pdb=" N ARG E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 86 through 89' Processing helix chain 'E' and resid 136 through 138 No H-bonds generated for 'chain 'E' and resid 136 through 138' Processing helix chain 'E' and resid 191 through 199 removed outlier: 4.147A pdb=" N SER E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU E 198 " --> pdb=" O GLU E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 225 removed outlier: 4.154A pdb=" N GLU E 218 " --> pdb=" O ALA E 214 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET E 219 " --> pdb=" O GLN E 215 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL E 220 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 230 No H-bonds generated for 'chain 'E' and resid 227 through 230' Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 281 through 295 removed outlier: 3.640A pdb=" N ARG E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU E 291 " --> pdb=" O ARG E 287 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 333 Processing helix chain 'E' and resid 355 through 358 Processing helix chain 'E' and resid 374 through 384 removed outlier: 3.566A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN E 382 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS E 384 " --> pdb=" O ILE E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 402 Processing helix chain 'E' and resid 408 through 426 removed outlier: 3.757A pdb=" N ALA E 412 " --> pdb=" O GLY E 408 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA E 422 " --> pdb=" O ALA E 418 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE E 423 " --> pdb=" O ALA E 419 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG E 424 " --> pdb=" O LEU E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 442 No H-bonds generated for 'chain 'E' and resid 439 through 442' Processing helix chain 'E' and resid 449 through 458 Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 483 through 491 removed outlier: 4.050A pdb=" N ARG E 487 " --> pdb=" O GLU E 483 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU E 488 " --> pdb=" O ASP E 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 498 No H-bonds generated for 'chain 'E' and resid 495 through 498' Processing helix chain 'E' and resid 500 through 506 removed outlier: 3.504A pdb=" N PHE E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 535 removed outlier: 3.844A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 552 removed outlier: 3.551A pdb=" N MET E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 568 removed outlier: 3.673A pdb=" N GLU E 561 " --> pdb=" O ASN E 558 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS E 565 " --> pdb=" O ILE E 562 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG E 567 " --> pdb=" O ASP E 564 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN E 568 " --> pdb=" O LYS E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 585 removed outlier: 4.452A pdb=" N ILE E 582 " --> pdb=" O LEU E 579 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS E 584 " --> pdb=" O SER E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 609 Processing helix chain 'E' and resid 626 through 628 No H-bonds generated for 'chain 'E' and resid 626 through 628' Processing helix chain 'E' and resid 631 through 633 No H-bonds generated for 'chain 'E' and resid 631 through 633' Processing helix chain 'E' and resid 650 through 660 removed outlier: 4.055A pdb=" N VAL E 654 " --> pdb=" O GLU E 650 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 678 removed outlier: 3.629A pdb=" N MET E 678 " --> pdb=" O PHE E 674 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 706 removed outlier: 3.512A pdb=" N GLU E 689 " --> pdb=" O ALA E 685 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE E 690 " --> pdb=" O ASP E 686 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 742 removed outlier: 4.110A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 750 through 763 removed outlier: 4.093A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR E 755 " --> pdb=" O ASP E 751 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 48 Processing helix chain 'F' and resid 86 through 89 removed outlier: 3.861A pdb=" N ARG F 89 " --> pdb=" O ARG F 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 86 through 89' Processing helix chain 'F' and resid 136 through 138 No H-bonds generated for 'chain 'F' and resid 136 through 138' Processing helix chain 'F' and resid 191 through 199 removed outlier: 4.147A pdb=" N SER F 197 " --> pdb=" O ASP F 193 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 225 removed outlier: 4.154A pdb=" N GLU F 218 " --> pdb=" O ALA F 214 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N MET F 219 " --> pdb=" O GLN F 215 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL F 220 " --> pdb=" O ILE F 216 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 227 through 230 No H-bonds generated for 'chain 'F' and resid 227 through 230' Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 281 through 295 removed outlier: 3.640A pdb=" N ARG F 287 " --> pdb=" O GLU F 283 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU F 291 " --> pdb=" O ARG F 287 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 333 Processing helix chain 'F' and resid 355 through 358 Processing helix chain 'F' and resid 374 through 384 removed outlier: 3.565A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN F 382 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS F 384 " --> pdb=" O ILE F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 402 Processing helix chain 'F' and resid 408 through 426 removed outlier: 3.757A pdb=" N ALA F 412 " --> pdb=" O GLY F 408 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA F 422 " --> pdb=" O ALA F 418 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE F 423 " --> pdb=" O ALA F 419 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG F 424 " --> pdb=" O LEU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 442 No H-bonds generated for 'chain 'F' and resid 439 through 442' Processing helix chain 'F' and resid 449 through 458 Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 483 through 491 removed outlier: 4.051A pdb=" N ARG F 487 " --> pdb=" O GLU F 483 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU F 488 " --> pdb=" O ASP F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 498 No H-bonds generated for 'chain 'F' and resid 495 through 498' Processing helix chain 'F' and resid 500 through 506 removed outlier: 3.504A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 535 removed outlier: 3.845A pdb=" N ALA F 528 " --> pdb=" O LYS F 524 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 552 removed outlier: 3.551A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 568 removed outlier: 3.673A pdb=" N GLU F 561 " --> pdb=" O ASN F 558 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS F 565 " --> pdb=" O ILE F 562 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG F 567 " --> pdb=" O ASP F 564 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN F 568 " --> pdb=" O LYS F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 579 through 585 removed outlier: 4.453A pdb=" N ILE F 582 " --> pdb=" O LEU F 579 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS F 584 " --> pdb=" O SER F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 609 Processing helix chain 'F' and resid 626 through 628 No H-bonds generated for 'chain 'F' and resid 626 through 628' Processing helix chain 'F' and resid 631 through 633 No H-bonds generated for 'chain 'F' and resid 631 through 633' Processing helix chain 'F' and resid 650 through 660 removed outlier: 4.055A pdb=" N VAL F 654 " --> pdb=" O GLU F 650 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 678 removed outlier: 3.629A pdb=" N MET F 678 " --> pdb=" O PHE F 674 " (cutoff:3.500A) Processing helix chain 'F' and resid 684 through 706 removed outlier: 3.511A pdb=" N GLU F 689 " --> pdb=" O ALA F 685 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE F 690 " --> pdb=" O ASP F 686 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 742 removed outlier: 4.111A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 750 through 763 removed outlier: 4.093A pdb=" N LYS F 754 " --> pdb=" O ASN F 750 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR F 755 " --> pdb=" O ASP F 751 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 58 through 60 removed outlier: 3.824A pdb=" N LEU A 58 " --> pdb=" O GLN A 103 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A 103 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 365 through 367 removed outlier: 8.973A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 641 through 645 removed outlier: 3.894A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 58 through 60 removed outlier: 3.825A pdb=" N LEU B 58 " --> pdb=" O GLN B 103 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN B 103 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 365 through 367 removed outlier: 8.973A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 641 through 645 removed outlier: 3.894A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.824A pdb=" N LEU C 58 " --> pdb=" O GLN C 103 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN C 103 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 365 through 367 removed outlier: 8.973A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 641 through 645 removed outlier: 3.894A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.824A pdb=" N LEU D 58 " --> pdb=" O GLN D 103 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN D 103 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 365 through 367 removed outlier: 8.973A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 641 through 645 removed outlier: 3.894A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.824A pdb=" N LEU E 58 " --> pdb=" O GLN E 103 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN E 103 " --> pdb=" O LEU E 58 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 365 through 367 removed outlier: 8.973A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 641 through 645 removed outlier: 3.894A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 58 through 60 removed outlier: 3.825A pdb=" N LEU F 58 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN F 103 " --> pdb=" O LEU F 58 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 365 through 367 removed outlier: 8.973A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 641 through 645 removed outlier: 3.894A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) 792 hydrogen bonds defined for protein. 2196 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.65 Time building geometry restraints manager: 13.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12013 1.34 - 1.46: 5005 1.46 - 1.58: 18484 1.58 - 1.69: 30 1.69 - 1.81: 288 Bond restraints: 35820 Sorted by residual: bond pdb=" C4 ADP B1002 " pdb=" C5 ADP B1002 " ideal model delta sigma weight residual 1.490 1.446 0.044 2.00e-02 2.50e+03 4.86e+00 bond pdb=" C4 ADP D1002 " pdb=" C5 ADP D1002 " ideal model delta sigma weight residual 1.490 1.446 0.044 2.00e-02 2.50e+03 4.82e+00 bond pdb=" C4 ADP E1002 " pdb=" C5 ADP E1002 " ideal model delta sigma weight residual 1.490 1.446 0.044 2.00e-02 2.50e+03 4.80e+00 bond pdb=" C4 ADP A1001 " pdb=" C5 ADP A1001 " ideal model delta sigma weight residual 1.490 1.446 0.044 2.00e-02 2.50e+03 4.80e+00 bond pdb=" C4 ADP A1002 " pdb=" C5 ADP A1002 " ideal model delta sigma weight residual 1.490 1.446 0.044 2.00e-02 2.50e+03 4.76e+00 ... (remaining 35815 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.85: 1283 106.85 - 114.08: 20689 114.08 - 121.31: 16869 121.31 - 128.55: 9429 128.55 - 135.78: 162 Bond angle restraints: 48432 Sorted by residual: angle pdb=" N ILE C 32 " pdb=" CA ILE C 32 " pdb=" C ILE C 32 " ideal model delta sigma weight residual 113.71 108.56 5.15 9.50e-01 1.11e+00 2.94e+01 angle pdb=" N ILE A 32 " pdb=" CA ILE A 32 " pdb=" C ILE A 32 " ideal model delta sigma weight residual 113.71 108.58 5.13 9.50e-01 1.11e+00 2.92e+01 angle pdb=" N ILE E 32 " pdb=" CA ILE E 32 " pdb=" C ILE E 32 " ideal model delta sigma weight residual 113.71 108.60 5.11 9.50e-01 1.11e+00 2.90e+01 angle pdb=" N ILE F 32 " pdb=" CA ILE F 32 " pdb=" C ILE F 32 " ideal model delta sigma weight residual 113.71 108.60 5.11 9.50e-01 1.11e+00 2.89e+01 angle pdb=" N ILE B 32 " pdb=" CA ILE B 32 " pdb=" C ILE B 32 " ideal model delta sigma weight residual 113.71 108.62 5.09 9.50e-01 1.11e+00 2.87e+01 ... (remaining 48427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.32: 21907 33.32 - 66.63: 207 66.63 - 99.95: 14 99.95 - 133.26: 10 133.26 - 166.58: 8 Dihedral angle restraints: 22146 sinusoidal: 9312 harmonic: 12834 Sorted by residual: dihedral pdb=" C5' ADP E1001 " pdb=" O5' ADP E1001 " pdb=" PA ADP E1001 " pdb=" O2A ADP E1001 " ideal model delta sinusoidal sigma weight residual -60.00 106.58 -166.58 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C5' ADP B1001 " pdb=" O5' ADP B1001 " pdb=" PA ADP B1001 " pdb=" O2A ADP B1001 " ideal model delta sinusoidal sigma weight residual -60.00 106.10 -166.10 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" O2A ADP E1001 " pdb=" O3A ADP E1001 " pdb=" PA ADP E1001 " pdb=" PB ADP E1001 " ideal model delta sinusoidal sigma weight residual -60.00 100.65 -160.65 1 2.00e+01 2.50e-03 4.66e+01 ... (remaining 22143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3458 0.037 - 0.074: 1465 0.074 - 0.110: 425 0.110 - 0.147: 94 0.147 - 0.184: 6 Chirality restraints: 5448 Sorted by residual: chirality pdb=" CG LEU E 420 " pdb=" CB LEU E 420 " pdb=" CD1 LEU E 420 " pdb=" CD2 LEU E 420 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.48e-01 chirality pdb=" CG LEU C 420 " pdb=" CB LEU C 420 " pdb=" CD1 LEU C 420 " pdb=" CD2 LEU C 420 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.30e-01 chirality pdb=" CG LEU D 420 " pdb=" CB LEU D 420 " pdb=" CD1 LEU D 420 " pdb=" CD2 LEU D 420 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.12e-01 ... (remaining 5445 not shown) Planarity restraints: 6354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 20 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C LYS D 20 " -0.030 2.00e-02 2.50e+03 pdb=" O LYS D 20 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN D 21 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 20 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C LYS B 20 " -0.030 2.00e-02 2.50e+03 pdb=" O LYS B 20 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN B 21 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 20 " 0.008 2.00e-02 2.50e+03 1.70e-02 2.91e+00 pdb=" C LYS A 20 " -0.029 2.00e-02 2.50e+03 pdb=" O LYS A 20 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN A 21 " 0.010 2.00e-02 2.50e+03 ... (remaining 6351 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3287 2.75 - 3.29: 35297 3.29 - 3.82: 54136 3.82 - 4.36: 64957 4.36 - 4.90: 106794 Nonbonded interactions: 264471 Sorted by model distance: nonbonded pdb=" O ASP E 669 " pdb=" NH2 ARG E 733 " model vdw 2.210 2.520 nonbonded pdb=" O ASP A 669 " pdb=" NH2 ARG A 733 " model vdw 2.211 2.520 nonbonded pdb=" O ASP F 669 " pdb=" NH2 ARG F 733 " model vdw 2.211 2.520 nonbonded pdb=" O ASP D 669 " pdb=" NH2 ARG D 733 " model vdw 2.211 2.520 nonbonded pdb=" O ASP C 669 " pdb=" NH2 ARG C 733 " model vdw 2.211 2.520 ... (remaining 264466 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 9.140 Check model and map are aligned: 0.460 Set scattering table: 0.330 Process input model: 89.570 Find NCS groups from input model: 2.390 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35820 Z= 0.221 Angle : 0.727 10.575 48432 Z= 0.392 Chirality : 0.044 0.184 5448 Planarity : 0.003 0.048 6354 Dihedral : 11.046 166.576 13830 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.13 % Favored : 91.60 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.13), residues: 4440 helix: -0.41 (0.13), residues: 1656 sheet: 0.68 (0.26), residues: 456 loop : -2.28 (0.12), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 454 HIS 0.002 0.001 HIS D 404 PHE 0.006 0.001 PHE E 773 TYR 0.009 0.001 TYR A 755 ARG 0.009 0.001 ARG E 567 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 4.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASN cc_start: 0.7145 (m110) cc_final: 0.6895 (m110) REVERT: B 332 MET cc_start: 0.8965 (tpp) cc_final: 0.8755 (tpp) REVERT: D 199 ASN cc_start: 0.7078 (m110) cc_final: 0.6835 (m110) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.4751 time to fit residues: 161.4345 Evaluate side-chains 169 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 4.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 40.0000 chunk 336 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 227 optimal weight: 0.0000 chunk 179 optimal weight: 4.9990 chunk 348 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 259 optimal weight: 0.8980 chunk 403 optimal weight: 6.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35820 Z= 0.214 Angle : 0.590 8.188 48432 Z= 0.273 Chirality : 0.044 0.154 5448 Planarity : 0.003 0.043 6354 Dihedral : 8.942 168.862 4962 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.02 % Favored : 91.71 % Rotamer: Outliers : 0.45 % Allowed : 4.01 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.13), residues: 4440 helix: -0.33 (0.12), residues: 1728 sheet: 0.74 (0.26), residues: 456 loop : -2.04 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 454 HIS 0.004 0.001 HIS A 340 PHE 0.014 0.001 PHE F 773 TYR 0.009 0.001 TYR F 755 ARG 0.004 0.000 ARG A 635 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 199 time to evaluate : 4.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASN cc_start: 0.7145 (m110) cc_final: 0.6889 (m110) REVERT: B 332 MET cc_start: 0.9168 (tpp) cc_final: 0.8910 (tpp) REVERT: D 199 ASN cc_start: 0.7105 (m110) cc_final: 0.6863 (m110) REVERT: E 199 ASN cc_start: 0.6930 (m110) cc_final: 0.6693 (m110) REVERT: E 332 MET cc_start: 0.9220 (tpp) cc_final: 0.9006 (tpp) REVERT: F 199 ASN cc_start: 0.7009 (m110) cc_final: 0.6779 (m110) outliers start: 17 outliers final: 9 residues processed: 202 average time/residue: 0.4214 time to fit residues: 149.0565 Evaluate side-chains 202 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 193 time to evaluate : 3.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 300 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 50.0000 chunk 125 optimal weight: 0.9990 chunk 335 optimal weight: 8.9990 chunk 274 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 403 optimal weight: 1.9990 chunk 436 optimal weight: 5.9990 chunk 359 optimal weight: 0.0870 chunk 400 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 324 optimal weight: 6.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 GLN C 348 ASN C 351 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 760 GLN E 348 ASN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 35820 Z= 0.253 Angle : 0.589 7.441 48432 Z= 0.275 Chirality : 0.044 0.132 5448 Planarity : 0.003 0.042 6354 Dihedral : 8.638 165.793 4962 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.86 % Favored : 91.89 % Rotamer: Outliers : 0.90 % Allowed : 6.41 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 4440 helix: -0.06 (0.13), residues: 1722 sheet: 0.92 (0.26), residues: 456 loop : -1.82 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 454 HIS 0.005 0.001 HIS F 340 PHE 0.019 0.002 PHE C 290 TYR 0.019 0.001 TYR D 244 ARG 0.005 0.000 ARG D 635 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 183 time to evaluate : 4.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASN cc_start: 0.7459 (m110) cc_final: 0.7142 (m110) REVERT: C 404 HIS cc_start: 0.8103 (OUTLIER) cc_final: 0.7886 (p-80) REVERT: D 199 ASN cc_start: 0.7127 (m110) cc_final: 0.6810 (m110) REVERT: F 404 HIS cc_start: 0.8080 (OUTLIER) cc_final: 0.7876 (p-80) outliers start: 34 outliers final: 21 residues processed: 204 average time/residue: 0.4202 time to fit residues: 150.4131 Evaluate side-chains 195 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 172 time to evaluate : 5.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 689 GLU Chi-restraints excluded: chain F residue 751 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 2.9990 chunk 303 optimal weight: 30.0000 chunk 209 optimal weight: 0.0270 chunk 44 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 chunk 271 optimal weight: 5.9990 chunk 405 optimal weight: 3.9990 chunk 429 optimal weight: 0.9980 chunk 211 optimal weight: 1.9990 chunk 384 optimal weight: 20.0000 chunk 115 optimal weight: 5.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN B 616 ASN D 616 ASN E 616 ASN F 616 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35820 Z= 0.219 Angle : 0.554 7.906 48432 Z= 0.254 Chirality : 0.044 0.133 5448 Planarity : 0.003 0.043 6354 Dihedral : 8.382 173.603 4962 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.84 % Favored : 92.03 % Rotamer: Outliers : 1.87 % Allowed : 5.96 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.13), residues: 4440 helix: 0.08 (0.13), residues: 1746 sheet: 0.96 (0.26), residues: 456 loop : -1.77 (0.14), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 454 HIS 0.004 0.001 HIS F 340 PHE 0.014 0.001 PHE F 265 TYR 0.011 0.001 TYR D 244 ARG 0.003 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 168 time to evaluate : 4.086 Fit side-chains REVERT: A 199 ASN cc_start: 0.7289 (m110) cc_final: 0.6941 (m110) REVERT: A 449 MET cc_start: 0.9077 (mmm) cc_final: 0.8635 (tpp) REVERT: C 420 LEU cc_start: 0.9313 (mt) cc_final: 0.9002 (tp) REVERT: D 199 ASN cc_start: 0.7155 (m110) cc_final: 0.6848 (m110) REVERT: D 449 MET cc_start: 0.9069 (mmm) cc_final: 0.8631 (tpp) REVERT: F 420 LEU cc_start: 0.9367 (mt) cc_final: 0.9003 (tp) REVERT: F 740 MET cc_start: 0.9744 (tpp) cc_final: 0.9495 (tpp) outliers start: 71 outliers final: 43 residues processed: 217 average time/residue: 0.4039 time to fit residues: 155.5928 Evaluate side-chains 199 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 156 time to evaluate : 4.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 731 ILE Chi-restraints excluded: chain F residue 751 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 5.9990 chunk 243 optimal weight: 3.9990 chunk 6 optimal weight: 50.0000 chunk 319 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 366 optimal weight: 1.9990 chunk 296 optimal weight: 60.0000 chunk 0 optimal weight: 50.0000 chunk 219 optimal weight: 5.9990 chunk 385 optimal weight: 0.4980 chunk 108 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 GLN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 35820 Z= 0.307 Angle : 0.604 11.850 48432 Z= 0.282 Chirality : 0.045 0.168 5448 Planarity : 0.003 0.044 6354 Dihedral : 7.473 163.858 4962 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.04 % Favored : 91.82 % Rotamer: Outliers : 1.87 % Allowed : 7.09 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.13), residues: 4440 helix: 0.08 (0.12), residues: 1782 sheet: 0.95 (0.26), residues: 456 loop : -1.77 (0.14), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 454 HIS 0.005 0.001 HIS A 226 PHE 0.017 0.002 PHE C 290 TYR 0.013 0.001 TYR E 244 ARG 0.005 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 168 time to evaluate : 5.215 Fit side-chains REVERT: A 199 ASN cc_start: 0.7490 (m110) cc_final: 0.7093 (m110) REVERT: C 420 LEU cc_start: 0.9388 (mt) cc_final: 0.9051 (tp) REVERT: E 740 MET cc_start: 0.9546 (mmm) cc_final: 0.9303 (mmm) REVERT: F 420 LEU cc_start: 0.9362 (mt) cc_final: 0.9040 (tp) outliers start: 71 outliers final: 53 residues processed: 222 average time/residue: 0.4136 time to fit residues: 161.0390 Evaluate side-chains 204 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 151 time to evaluate : 3.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 351 ASN Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 598 ASP Chi-restraints excluded: chain F residue 689 GLU Chi-restraints excluded: chain F residue 731 ILE Chi-restraints excluded: chain F residue 751 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 6.9990 chunk 386 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 429 optimal weight: 0.9990 chunk 356 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 225 optimal weight: 50.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35820 Z= 0.223 Angle : 0.570 11.061 48432 Z= 0.261 Chirality : 0.044 0.163 5448 Planarity : 0.003 0.044 6354 Dihedral : 7.051 163.758 4962 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.88 % Favored : 91.94 % Rotamer: Outliers : 2.16 % Allowed : 8.02 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.13), residues: 4440 helix: 0.20 (0.12), residues: 1782 sheet: 1.02 (0.26), residues: 438 loop : -1.73 (0.14), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 454 HIS 0.004 0.001 HIS F 340 PHE 0.014 0.001 PHE A 363 TYR 0.011 0.001 TYR A 244 ARG 0.003 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 158 time to evaluate : 4.069 Fit side-chains REVERT: A 199 ASN cc_start: 0.7478 (m110) cc_final: 0.7071 (m110) REVERT: A 438 ASP cc_start: 0.6388 (OUTLIER) cc_final: 0.5695 (p0) REVERT: B 438 ASP cc_start: 0.6497 (OUTLIER) cc_final: 0.6122 (p0) REVERT: B 740 MET cc_start: 0.9571 (mmm) cc_final: 0.9330 (mmm) REVERT: C 420 LEU cc_start: 0.9367 (mt) cc_final: 0.9086 (tp) REVERT: D 438 ASP cc_start: 0.6305 (OUTLIER) cc_final: 0.5548 (p0) REVERT: E 438 ASP cc_start: 0.6297 (OUTLIER) cc_final: 0.5912 (p0) REVERT: E 740 MET cc_start: 0.9564 (mmm) cc_final: 0.9310 (mmm) REVERT: F 420 LEU cc_start: 0.9354 (mt) cc_final: 0.9076 (tp) outliers start: 82 outliers final: 59 residues processed: 217 average time/residue: 0.3950 time to fit residues: 152.0571 Evaluate side-chains 216 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 153 time to evaluate : 4.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 351 ASN Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 731 ILE Chi-restraints excluded: chain F residue 751 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 244 optimal weight: 0.8980 chunk 313 optimal weight: 9.9990 chunk 243 optimal weight: 1.9990 chunk 361 optimal weight: 2.9990 chunk 239 optimal weight: 9.9990 chunk 427 optimal weight: 0.1980 chunk 267 optimal weight: 0.5980 chunk 260 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 HIS ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 HIS ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35820 Z= 0.220 Angle : 0.565 10.723 48432 Z= 0.258 Chirality : 0.044 0.170 5448 Planarity : 0.003 0.044 6354 Dihedral : 6.813 164.465 4962 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.04 % Favored : 91.82 % Rotamer: Outliers : 2.27 % Allowed : 8.15 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.13), residues: 4440 helix: 0.27 (0.12), residues: 1788 sheet: 1.10 (0.26), residues: 438 loop : -1.70 (0.14), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 454 HIS 0.005 0.001 HIS D 340 PHE 0.016 0.001 PHE A 363 TYR 0.020 0.001 TYR E 244 ARG 0.005 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 156 time to evaluate : 3.831 Fit side-chains REVERT: A 154 VAL cc_start: 0.1361 (OUTLIER) cc_final: 0.1044 (p) REVERT: A 199 ASN cc_start: 0.7518 (m110) cc_final: 0.7092 (m110) REVERT: A 438 ASP cc_start: 0.6428 (OUTLIER) cc_final: 0.5736 (p0) REVERT: A 449 MET cc_start: 0.8835 (tpp) cc_final: 0.8431 (tpp) REVERT: B 438 ASP cc_start: 0.6399 (OUTLIER) cc_final: 0.6012 (p0) REVERT: B 740 MET cc_start: 0.9584 (mmm) cc_final: 0.9337 (mmm) REVERT: C 420 LEU cc_start: 0.9372 (mt) cc_final: 0.9089 (tp) REVERT: D 154 VAL cc_start: 0.1390 (OUTLIER) cc_final: 0.1076 (p) REVERT: D 438 ASP cc_start: 0.6335 (OUTLIER) cc_final: 0.5585 (p0) REVERT: D 449 MET cc_start: 0.8828 (tpp) cc_final: 0.8445 (tpp) REVERT: E 438 ASP cc_start: 0.6220 (OUTLIER) cc_final: 0.5825 (p0) REVERT: E 740 MET cc_start: 0.9588 (mmm) cc_final: 0.9326 (mmm) REVERT: F 420 LEU cc_start: 0.9359 (mt) cc_final: 0.9079 (tp) outliers start: 86 outliers final: 64 residues processed: 226 average time/residue: 0.3883 time to fit residues: 157.6529 Evaluate side-chains 220 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 150 time to evaluate : 5.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 351 ASN Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 598 ASP Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 731 ILE Chi-restraints excluded: chain F residue 751 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 0.2980 chunk 170 optimal weight: 2.9990 chunk 255 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 82 optimal weight: 30.0000 chunk 272 optimal weight: 0.0270 chunk 291 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 336 optimal weight: 2.9990 overall best weight: 2.0644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 382 GLN ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 382 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 382 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 35820 Z= 0.299 Angle : 0.600 7.891 48432 Z= 0.279 Chirality : 0.045 0.166 5448 Planarity : 0.003 0.045 6354 Dihedral : 6.913 165.818 4962 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.81 % Favored : 91.13 % Rotamer: Outliers : 2.40 % Allowed : 8.02 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.13), residues: 4440 helix: 0.17 (0.12), residues: 1824 sheet: 1.02 (0.26), residues: 456 loop : -1.70 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 454 HIS 0.004 0.001 HIS E 226 PHE 0.016 0.001 PHE A 363 TYR 0.022 0.001 TYR F 244 ARG 0.005 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 156 time to evaluate : 4.063 Fit side-chains REVERT: A 154 VAL cc_start: 0.1442 (OUTLIER) cc_final: 0.1112 (p) REVERT: A 199 ASN cc_start: 0.7557 (m110) cc_final: 0.7124 (m110) REVERT: A 438 ASP cc_start: 0.6566 (OUTLIER) cc_final: 0.5795 (p0) REVERT: A 449 MET cc_start: 0.8781 (tpp) cc_final: 0.8298 (tpp) REVERT: B 332 MET cc_start: 0.9313 (tpp) cc_final: 0.8858 (tpt) REVERT: B 438 ASP cc_start: 0.6245 (OUTLIER) cc_final: 0.5823 (p0) REVERT: B 740 MET cc_start: 0.9607 (mmm) cc_final: 0.9329 (mmm) REVERT: C 420 LEU cc_start: 0.9399 (mt) cc_final: 0.9101 (tp) REVERT: D 154 VAL cc_start: 0.1466 (OUTLIER) cc_final: 0.1139 (p) REVERT: D 199 ASN cc_start: 0.7493 (m110) cc_final: 0.7052 (m110) REVERT: D 438 ASP cc_start: 0.6725 (OUTLIER) cc_final: 0.5902 (p0) REVERT: D 449 MET cc_start: 0.8773 (tpp) cc_final: 0.8302 (tpp) REVERT: E 438 ASP cc_start: 0.6418 (OUTLIER) cc_final: 0.6001 (p0) REVERT: E 740 MET cc_start: 0.9612 (mmm) cc_final: 0.9323 (mmm) REVERT: F 420 LEU cc_start: 0.9394 (mt) cc_final: 0.9083 (tp) REVERT: F 438 ASP cc_start: 0.6510 (OUTLIER) cc_final: 0.6291 (p0) outliers start: 91 outliers final: 73 residues processed: 224 average time/residue: 0.4035 time to fit residues: 162.1656 Evaluate side-chains 233 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 153 time to evaluate : 3.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 689 GLU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 351 ASN Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 438 ASP Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 598 ASP Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 689 GLU Chi-restraints excluded: chain F residue 731 ILE Chi-restraints excluded: chain F residue 751 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 0.2980 chunk 409 optimal weight: 1.9990 chunk 374 optimal weight: 0.2980 chunk 398 optimal weight: 0.6980 chunk 240 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 chunk 313 optimal weight: 0.3980 chunk 122 optimal weight: 0.9980 chunk 360 optimal weight: 4.9990 chunk 377 optimal weight: 9.9990 chunk 397 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN C 382 GLN F 382 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 35820 Z= 0.154 Angle : 0.547 10.802 48432 Z= 0.249 Chirality : 0.043 0.175 5448 Planarity : 0.003 0.045 6354 Dihedral : 6.540 166.155 4962 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.96 % Favored : 93.02 % Rotamer: Outliers : 1.40 % Allowed : 9.15 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.13), residues: 4440 helix: 0.36 (0.12), residues: 1818 sheet: 1.19 (0.26), residues: 438 loop : -1.63 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 454 HIS 0.005 0.001 HIS A 340 PHE 0.011 0.001 PHE F 363 TYR 0.011 0.001 TYR D 244 ARG 0.006 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 168 time to evaluate : 4.295 Fit side-chains REVERT: A 154 VAL cc_start: 0.1382 (OUTLIER) cc_final: 0.1046 (p) REVERT: A 199 ASN cc_start: 0.7494 (m110) cc_final: 0.7061 (m110) REVERT: A 438 ASP cc_start: 0.6563 (OUTLIER) cc_final: 0.5853 (p0) REVERT: A 449 MET cc_start: 0.8754 (tpp) cc_final: 0.8387 (tpp) REVERT: B 438 ASP cc_start: 0.6512 (OUTLIER) cc_final: 0.6144 (p0) REVERT: B 740 MET cc_start: 0.9588 (mmm) cc_final: 0.9353 (mmm) REVERT: C 420 LEU cc_start: 0.9374 (mt) cc_final: 0.9082 (tp) REVERT: C 438 ASP cc_start: 0.6586 (OUTLIER) cc_final: 0.6122 (p0) REVERT: D 154 VAL cc_start: 0.1464 (OUTLIER) cc_final: 0.1131 (p) REVERT: D 438 ASP cc_start: 0.6373 (OUTLIER) cc_final: 0.5667 (p0) REVERT: D 449 MET cc_start: 0.8749 (tpp) cc_final: 0.8386 (tpp) REVERT: E 438 ASP cc_start: 0.6332 (OUTLIER) cc_final: 0.5939 (p0) REVERT: E 740 MET cc_start: 0.9601 (mmm) cc_final: 0.9347 (mmm) REVERT: F 420 LEU cc_start: 0.9359 (mt) cc_final: 0.9069 (tp) outliers start: 53 outliers final: 36 residues processed: 212 average time/residue: 0.4168 time to fit residues: 156.3870 Evaluate side-chains 199 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 156 time to evaluate : 3.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 598 ASP Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 751 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 7.9990 chunk 421 optimal weight: 0.9990 chunk 257 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 293 optimal weight: 0.7980 chunk 442 optimal weight: 4.9990 chunk 407 optimal weight: 0.0270 chunk 352 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 272 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35820 Z= 0.202 Angle : 0.564 11.035 48432 Z= 0.258 Chirality : 0.044 0.171 5448 Planarity : 0.003 0.045 6354 Dihedral : 6.540 167.195 4962 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.73 % Favored : 92.23 % Rotamer: Outliers : 1.45 % Allowed : 9.34 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.13), residues: 4440 helix: 0.41 (0.12), residues: 1818 sheet: 1.21 (0.26), residues: 438 loop : -1.61 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 454 HIS 0.005 0.001 HIS E 340 PHE 0.014 0.001 PHE C 363 TYR 0.022 0.001 TYR A 244 ARG 0.007 0.000 ARG A 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 163 time to evaluate : 4.044 Fit side-chains REVERT: A 154 VAL cc_start: 0.1407 (OUTLIER) cc_final: 0.1072 (p) REVERT: A 199 ASN cc_start: 0.7572 (m110) cc_final: 0.7139 (m110) REVERT: A 438 ASP cc_start: 0.6610 (OUTLIER) cc_final: 0.5849 (p0) REVERT: A 449 MET cc_start: 0.8740 (tpp) cc_final: 0.8373 (tpp) REVERT: B 388 MET cc_start: 0.9020 (ptt) cc_final: 0.8720 (ptt) REVERT: B 438 ASP cc_start: 0.6572 (OUTLIER) cc_final: 0.6202 (p0) REVERT: B 740 MET cc_start: 0.9603 (mmm) cc_final: 0.9346 (mmm) REVERT: C 420 LEU cc_start: 0.9379 (mt) cc_final: 0.9088 (tp) REVERT: C 438 ASP cc_start: 0.6633 (OUTLIER) cc_final: 0.6416 (p0) REVERT: D 154 VAL cc_start: 0.1479 (OUTLIER) cc_final: 0.1147 (p) REVERT: D 244 TYR cc_start: 0.7281 (m-80) cc_final: 0.6927 (t80) REVERT: D 438 ASP cc_start: 0.6503 (OUTLIER) cc_final: 0.5739 (p0) REVERT: D 449 MET cc_start: 0.8735 (tpp) cc_final: 0.8385 (tpp) REVERT: E 438 ASP cc_start: 0.6167 (OUTLIER) cc_final: 0.5773 (p0) REVERT: E 740 MET cc_start: 0.9605 (mmm) cc_final: 0.9331 (mmm) REVERT: F 420 LEU cc_start: 0.9374 (mt) cc_final: 0.9073 (tp) outliers start: 55 outliers final: 45 residues processed: 210 average time/residue: 0.4132 time to fit residues: 153.1174 Evaluate side-chains 211 residues out of total 3798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 159 time to evaluate : 3.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 598 ASP Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 598 ASP Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 689 GLU Chi-restraints excluded: chain F residue 751 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 3.9990 chunk 375 optimal weight: 30.0000 chunk 107 optimal weight: 2.9990 chunk 324 optimal weight: 0.0670 chunk 52 optimal weight: 0.7980 chunk 97 optimal weight: 0.0980 chunk 352 optimal weight: 0.7980 chunk 147 optimal weight: 10.0000 chunk 362 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 HIS D 406 HIS ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.144663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.085364 restraints weight = 69369.460| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 4.82 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35820 Z= 0.183 Angle : 0.553 10.619 48432 Z= 0.252 Chirality : 0.044 0.171 5448 Planarity : 0.003 0.045 6354 Dihedral : 6.482 168.085 4962 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 1.45 % Allowed : 9.44 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.13), residues: 4440 helix: 0.43 (0.12), residues: 1818 sheet: 1.22 (0.27), residues: 438 loop : -1.59 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 454 HIS 0.003 0.001 HIS B 340 PHE 0.015 0.001 PHE C 363 TYR 0.020 0.001 TYR E 244 ARG 0.006 0.000 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5674.87 seconds wall clock time: 105 minutes 10.71 seconds (6310.71 seconds total)